Scientific

MK5 Microarray Data


Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

  • value_type as 'ranked' since this provides a very robust analysis method.
  • intercation map as 'high confidence'
  • network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins
  • filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

  • Navigation/Query Panel:
    Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
    Filtered Value Type Network Comparison Type Gene green red network_comparison Interaction Map Rank description
    Results: HTML CSV LaTeX Showing element 1 to 50 of 77072 in total
    Filtered  : 0
    Value Type  : Measured
    Network Comparison Type  : Divided
    green
    red
    network_comparison
    Interaction Map
    Rank
    description
    0.00001 0.00001 1 High confidence 494 histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]
    495 histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001]
    496 mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932]
    497 histone h2a; h2a histone family, member r. [refseq;acc:nm_170745]
    498 translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]
    499 homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]
    500 rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952]
    501 h2a histone family, member j isoform 1. [refseq;acc:nm_018267]
    502 brca1 associated protein. [refseq;acc:nm_006768]
    Low confidence 837 gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [swissprot;acc:p36268]
    838 gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [refseq;acc:nm_080920]
    839 cobw-like protein. [refseq;acc:nm_018491]
    840 translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]
    841 gamma-glutamyltransferase. [sptrembl;acc:q14390]
    842 gamma-glutamyltranspeptidase 1 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 1) (cd224 antigen). [swissprot;acc:p19440]
    843 gamma-glutamyltranspeptidase 5 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 5) (ggt-rel). [swissprot;acc:p36269]
    2.31962 231962 7 tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063]
    13 1300000 6 homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]
    18 1800000 High confidence 65 rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]
    35 3500000 31 dok-like protein. [refseq;acc:nm_024872]
    37 3700000 Low confidence 22 carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615]
    23 carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]
    60 6000000 High confidence 22 similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]
    82 8200000 20 ero1-like. [refseq;acc:nm_014584]
    154 15400000 95 nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]
    96 transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]
    286 28600000 Low confidence 44 neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]
    45 neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]
    364 36400000 High confidence 1 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]
    Low confidence
    5.56738 199.549 35.8425 High confidence 11 serpin b12. [swissprot;acc:q96p63]
    Low confidence 10
    5.71669 199.249 34.8539 High confidence 12 hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]
    Low confidence 11
    6.50325 130.512 20.0687 High confidence 14 cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]
    10.6048 383.762 36.1876 Low confidence 9 ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607]
    11.5 14 1.21739 High confidence 190 protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0]
    Low confidence 176
    14.3333 19.6667 1.3721 High confidence 121 4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404]
    15 1 15 16 protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]
    17.5166 0.00001 1751660 Low confidence 5 jumonji protein. [swissprot;acc:q92833]
    17.6611 118.878 6.73106 High confidence 21 syntaxin 10 (syn10). [swissprot;acc:o60499]
    18 0.00001 1800000 64 phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750]
    19 23 1.21053 195 adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559]
    Low confidence 184
    99 5.21053 18 camp-regulated phosphoprotein 19 (arpp-19) [contains: camp-regulated phosphoprotein 16 (arpp-16)]. [swissprot;acc:p56211]
    21 44 2.09524 High confidence 50 transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884]
    23.6984 48.2534 2.03615 Low confidence 64 dna helicase homolog (fragment). [sptrembl;acc:q9y645]
    26.1599 305.45 11.6763 High confidence 18 60s ribosomal protein l37a. [swissprot;acc:p12751]
    19 25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528]

    Legend:
    - Rank is the rank after comparing the two networks
    - Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
    - Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
    - Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
    - Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
    - Filtered specifies whether we only included the high confidence microarry measurements or not.

    - http://analysis.yellowcouch.org/